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Yorodumi- PDB-6pd1: PntC-AEPT: fusion protein of phosphonate-specific cytidylyltransf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pd1 | ||||||
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Title | PntC-AEPT: fusion protein of phosphonate-specific cytidylyltransferase and 2-aminoethylphosphonate (AEP) transaminase from Treponema denticola | ||||||
Components | Nucleotidyl transferase/aminotransferase, class V | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Phosphonate / Cytidylyltransferase / Cytidine monophosphate- 2-aminoethylphosphonate (CMP-AEP) | ||||||
Function / homology | Function and homology information 2-aminoethylphosphonate-pyruvate transaminase activity / organic phosphonate catabolic process Similarity search - Function | ||||||
Biological species | Treponema denticola (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å | ||||||
Authors | Suits, M.D.L. / Whiteside, J. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: The predominance of nucleotidyl activation in bacterial phosphonate biosynthesis. Authors: Rice, K. / Batul, K. / Whiteside, J. / Kelso, J. / Papinski, M. / Schmidt, E. / Pratasouskaya, A. / Wang, D. / Sullivan, R. / Bartlett, C. / Weadge, J.T. / Van der Kamp, M.W. / Moreno- ...Authors: Rice, K. / Batul, K. / Whiteside, J. / Kelso, J. / Papinski, M. / Schmidt, E. / Pratasouskaya, A. / Wang, D. / Sullivan, R. / Bartlett, C. / Weadge, J.T. / Van der Kamp, M.W. / Moreno-Hagelsieb, G. / Suits, M.D. / Horsman, G.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pd1.cif.gz | 482.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pd1.ent.gz | 392.2 KB | Display | PDB format |
PDBx/mmJSON format | 6pd1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pd/6pd1 ftp://data.pdbj.org/pub/pdb/validation_reports/pd/6pd1 | HTTPS FTP |
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-Related structure data
Related structure data | 6pd2C 1jykS 1vjoS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 70148.680 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Treponema denticola (strain ATCC 35405 / CIP 103919 / DSM 14222) (bacteria) Strain: ATCC 35405 / CIP 103919 / DSM 14222 / Gene: TDE_1415 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q73MU2 |
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-Non-polymers , 6 types, 195 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-NI / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.01 M nickel II chloride hexahydrate, 0.1 M Tris-HCl, pH 8.5, 1.0 M lithium sulfate monohydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.72→38 Å / Num. obs: 82344 / % possible obs: 99.8 % / Redundancy: 4.2 % / CC1/2: 0.996 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.72→2.77 Å / Num. unique obs: 4114 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JYK, 1VJO Resolution: 2.72→38 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.33
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.72→38 Å
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Refine LS restraints |
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LS refinement shell |
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